Bug 2253360

Summary:

Review Request: papilo - Parallel presolve for integer and linear optimization

Product:

[Fedora] Fedora

Reporter:

Jerry James <loganjerry>

Component:

Package Review

Assignee:

Benson Muite <benson_muite>

Status:

CLOSED NEXTRELEASE

QA Contact:

Fedora Extras Quality Assurance <extras-qa>

Severity:

medium

Docs Contact:

Priority:

medium

Version:

rawhide

CC:

benson_muite, package-review

Target Milestone:

---

Flags:

benson_muite: fedora-review+

Target Release:

---

Hardware:

All

OS:

Linux

URL:

https://github.com/scipopt/papilo/

Whiteboard:

Fixed In Version:

Doc Type:

If docs needed, set a value

Doc Text:

Story Points:

---

Clone Of:

Environment:

Last Closed:

2024-02-16 03:54:49 UTC

Type:

---

Regression:

---

Mount Type:

---

Documentation:

---

CRM:

Verified Versions:

Category:

---

oVirt Team:

---

RHEL 7.3 requirements from Atomic Host:

Cloudforms Team:

---

Target Upstream Version:

Embargoed:

Bug Depends On:

2253356, 2253357

Bug Blocks:

2253361

Attachments:

Description	Flags
The .spec file difference from Copr build 7010715 to 7018192	none

Description Jerry James 2023-12-06 21:46:33 UTC

Spec URL: https://jjames.fedorapeople.org/papilo/papilo.spec
SRPM URL: https://jjames.fedorapeople.org/papilo/papilo-2.1.4-1.fc40.src.rpm
Fedora Account System Username: jjames
Description: PaPILO provides parallel presolve routines for (mixed integer) linear programming problems.  The routines are implemented using templates which allows switching to higher precision or rational arithmetic using the boost multiprecision package.

This package is part of an effort to add the SoPlex and SCIP solvers to Fedora.  The entire collection of packages is available in a COPR: https://copr.fedorainfracloud.org/coprs/jjames/SCIP/.  To do a mock build of this package, create ~/.config/mock/fedora-scip-x86_64.cfg with the following contents, then run "mock -r fedora-scip-x86_64" or "fedora-review -m fedora-scip-x86_64".

include('/etc/mock/fedora-rawhide-x86_64.cfg')

config_opts['root'] = 'fedora-rawhide-scip'

config_opts[f'{config_opts.package_manager}.conf'] += """

[scip]
name=Copr repo for SCIP owned by jjames
baseurl=https://copr-be.cloud.fedoraproject.org/results/jjames/SCIP/fedora-rawhide-$basearch/
type=rpm-md
skip_if_unavailable=False
gpgcheck=1
gpgkey=https://copr-be.cloud.fedoraproject.org/results/jjames/SCIP/pubkey.gpg
repo_gpgcheck=0
enabled=1
enabled_metadata=1
cost=10
"""

Comment 1 Fedora Review Service 2023-12-06 21:49:55 UTC

Copr build:
https://copr.fedorainfracloud.org/coprs/build/6729880
(failed)

Build log:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2253360-papilo/fedora-rawhide-x86_64/06729880-papilo/builder-live.log.gz

Please make sure the package builds successfully at least for Fedora Rawhide.

- If the build failed for unrelated reasons (e.g. temporary network
  unavailability), please ignore it.
- If the build failed because of missing BuildRequires, please make sure they
  are listed in the "Depends On" field


---
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If you want to trigger a new Copr build, add a comment containing new
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Comment 2 Jerry James 2024-02-09 21:22:39 UTC

[fedora-review-service-build]

Comment 3 Fedora Review Service 2024-02-10 05:12:00 UTC

Copr build:
https://copr.fedorainfracloud.org/coprs/build/7005488
(failed)

Build log:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2253360-papilo/fedora-rawhide-x86_64/07005488-papilo/builder-live.log.gz

Please make sure the package builds successfully at least for Fedora Rawhide.

- If the build failed for unrelated reasons (e.g. temporary network
  unavailability), please ignore it.
- If the build failed because of missing BuildRequires, please make sure they
  are listed in the "Depends On" field


---
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If you want to trigger a new Copr build, add a comment containing new
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Comment 4 Jerry James 2024-02-12 15:42:12 UTC

[fedora-review-service-build]

Comment 5 Fedora Review Service 2024-02-13 00:14:56 UTC

Copr build:
https://copr.fedorainfracloud.org/coprs/build/7010715
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2253360-papilo/fedora-rawhide-x86_64/07010715-papilo/fedora-review/review.txt

Please take a look if any issues were found.


---
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If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 6 Benson Muite 2024-02-14 09:38:52 UTC

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed



===== MUST items =====

C/C++:
[-]: Provides: bundled(gnulib) in place as required.
     Note: Sources not installed
[x]: Package does not contain kernel modules.
[x]: If your application is a C or C++ application you must list a
     BuildRequires against gcc, gcc-c++ or clang.
[x]: Header files in -devel subpackage, if present.
[x]: ldconfig not called in %post and %postun for Fedora 28 and later.
[x]: Package does not contain any libtool archives (.la)
[x]: Package contains no static executables.
[x]: Rpath absent or only used for internal libs.
[x]: Development (unversioned) .so files in -devel subpackage, if present.

Generic:
[x]: Package is licensed with an open-source compatible license and meets
     other legal requirements as defined in the legal section of Packaging
     Guidelines.
[!]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "Unknown or generated", "GNU Lesser General Public License,
     Version 3", "*No copyright* GNU Lesser General Public License, Version
     3", "GNU Lesser General Public License v3.0 or later", "Apache License
     2.0", "Boost Software License 1.0", "MIT License", "*No copyright* MIT
     License". 132 files have unknown license. Detailed output of
     licensecheck in /home/fedora/2253360-papilo/licensecheck.txt
[!]: License file installed when any subpackage combination is installed.
[ ]: If the package is under multiple licenses, the licensing breakdown
     must be documented in the spec.
[ ]: Package requires other packages for directories it uses.
     Note: No known owner of /usr/lib64/cmake
[x]: %build honors applicable compiler flags or justifies otherwise.
[ ]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[-]: Package contains desktop file if it is a GUI application.
[x]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.
[x]: Package does not generate any conflict.
[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[x]: Useful -debuginfo package or justification otherwise.
[x]: Package is not known to require an ExcludeArch tag.
[-]: Large documentation must go in a -doc subpackage. Large could be size
     (~1MB) or number of files.
     Note: Documentation size is 46255 bytes in 3 files.
[x]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[x]: Package installs properly.
[x]: Rpmlint is run on all rpms the build produces.
     Note: There are rpmlint messages (see attachment).
[x]: If (and only if) the source package includes the text of the
     license(s) in its own file, then that file, containing the text of the
     license(s) for the package is included in %license.
[x]: The License field must be a valid SPDX expression.
[x]: Package must own all directories that it creates.
[x]: Package does not own files or directories owned by other packages.
[x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT
[x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the
     beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package must not depend on deprecated() packages.
[x]: Package use %makeinstall only when make install DESTDIR=... doesn't
     work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package does not use a name that already exists.
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as
     provided in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
     %{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files under /srv, /opt or /usr/local

===== SHOULD items =====

Generic:
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[ ]: Fully versioned dependency in subpackages if applicable.
     Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in
     libpapilo
[ ]: Package functions as described.
[x]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[x]: Patches link to upstream bugs/comments/lists or are otherwise
     justified.
[-]: Sources are verified with gpgverify first in %prep if upstream
     publishes signatures.
     Note: gpgverify is not used.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[x]: Packages should try to preserve timestamps of original installed
     files.
[x]: Reviewer should test that the package builds in mock.
[x]: Buildroot is not present
[x]: Package has no %clean section with rm -rf %{buildroot} (or
     $RPM_BUILD_ROOT)
[x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file
[x]: Sources can be downloaded from URI in Source: tag
[x]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[x]: Rpmlint is run on debuginfo package(s).
     Note: No rpmlint messages.
[x]: Rpmlint is run on all installed packages.
     Note: There are rpmlint messages (see attachment).
[x]: Large data in /usr/share should live in a noarch subpackage if package
     is arched.
[x]: Spec file according to URL is the same as in SRPM.


Rpmlint
-------
Checking: papilo-2.1.4-1.fc40.x86_64.rpm
          libpapilo-2.1.4-1.fc40.x86_64.rpm
          libpapilo-devel-2.1.4-1.fc40.x86_64.rpm
          papilo-debuginfo-2.1.4-1.fc40.x86_64.rpm
          papilo-debugsource-2.1.4-1.fc40.x86_64.rpm
          papilo-2.1.4-1.fc40.src.rpm
============================ rpmlint session starts ============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmpzdtiemx4')]
checks: 32, packages: 6

libpapilo.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
libpapilo-devel.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
papilo.src: E: spelling-error ('presolve', 'Summary(en_US) presolve -> resolve, p resolve, preserve')
papilo.src: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
papilo.x86_64: E: spelling-error ('presolve', 'Summary(en_US) presolve -> resolve, p resolve, preserve')
papilo.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
papilo.x86_64: W: no-manual-page-for-binary duplicates
papilo.x86_64: W: no-manual-page-for-binary papilo
 6 packages and 0 specfiles checked; 6 errors, 2 warnings, 42 filtered, 6 badness; has taken 1.7 s 




Rpmlint (debuginfo)
-------------------
Checking: papilo-debuginfo-2.1.4-1.fc40.x86_64.rpm
============================ rpmlint session starts ============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
rpmlintrc: [PosixPath('/tmp/tmpd_0zqlt4')]
checks: 32, packages: 1

 1 packages and 0 specfiles checked; 0 errors, 0 warnings, 12 filtered, 0 badness; has taken 0.5 s 





Rpmlint (installed packages)
----------------------------
============================ rpmlint session starts ============================
rpmlint: 2.5.0
configuration:
    /usr/lib/python3.12/site-packages/rpmlint/configdefaults.toml
    /etc/xdg/rpmlint/fedora-legacy-licenses.toml
    /etc/xdg/rpmlint/fedora-spdx-licenses.toml
    /etc/xdg/rpmlint/fedora.toml
    /etc/xdg/rpmlint/scoring.toml
    /etc/xdg/rpmlint/users-groups.toml
    /etc/xdg/rpmlint/warn-on-functions.toml
checks: 32, packages: 5

libpapilo.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
papilo.x86_64: E: spelling-error ('presolve', 'Summary(en_US) presolve -> resolve, p resolve, preserve')
papilo.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
libpapilo-devel.x86_64: E: spelling-error ('presolve', '%description -l en_US presolve -> resolve, p resolve, preserve')
papilo.x86_64: W: no-manual-page-for-binary duplicates
papilo.x86_64: W: no-manual-page-for-binary papilo
 5 packages and 0 specfiles checked; 4 errors, 2 warnings, 39 filtered, 4 badness; has taken 1.4 s 



Source checksums
----------------
https://github.com/scipopt/papilo//archive/v2.1.4/papilo-2.1.4.tar.gz :
  CHECKSUM(SHA256) this package     : 3526f3f9a6036c4b51f324f24535b5ee63e26cbc5d3f893a765cbc9cd721fac9
  CHECKSUM(SHA256) upstream package : 3526f3f9a6036c4b51f324f24535b5ee63e26cbc5d3f893a765cbc9cd721fac9


Requires
--------
papilo (rpmlib, GLIBC filtered):
    libboost_iostreams.so.1.83.0()(64bit)
    libboost_program_options.so.1.83.0()(64bit)
    libboost_serialization.so.1.83.0()(64bit)
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_3.3.1)(64bit)
    libgcc_s.so.1(GCC_4.3.0)(64bit)
    libgmp.so.10()(64bit)
    libm.so.6()(64bit)
    libpapilo(x86-64)
    libpapilo-core.so.0()(64bit)
    libquadmath.so.0()(64bit)
    libquadmath.so.0(QUADMATH_1.0)(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.15)(64bit)
    libstdc++.so.6(CXXABI_1.3.5)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libtbb.so.12()(64bit)
    rtld(GNU_HASH)

libpapilo (rpmlib, GLIBC filtered):
    libc.so.6()(64bit)
    libclusol.so.0()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libgcc_s.so.1(GCC_3.3.1)(64bit)
    libgcc_s.so.1(GCC_4.3.0)(64bit)
    libgmp.so.10()(64bit)
    libm.so.6()(64bit)
    libquadmath.so.0()(64bit)
    libquadmath.so.0(QUADMATH_1.0)(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    libstdc++.so.6(CXXABI_1.3.5)(64bit)
    libstdc++.so.6(CXXABI_1.3.8)(64bit)
    libstdc++.so.6(CXXABI_1.3.9)(64bit)
    libtbb.so.12()(64bit)
    rtld(GNU_HASH)

libpapilo-devel (rpmlib, GLIBC filtered):
    boost-devel(x86-64)
    cmake-filesystem(x86-64)
    libpapilo(x86-64)
    libpapilo-core.so.0()(64bit)
    lusol-devel(x86-64)
    pdqsort-static
    tbb-devel(x86-64)

papilo-debuginfo (rpmlib, GLIBC filtered):

papilo-debugsource (rpmlib, GLIBC filtered):



Provides
--------
papilo:
    bundled(fmt)
    papilo
    papilo(x86-64)

libpapilo:
    libpapilo
    libpapilo(x86-64)
    libpapilo-core.so.0()(64bit)

libpapilo-devel:
    cmake(papilo)
    libpapilo-devel
    libpapilo-devel(x86-64)

papilo-debuginfo:
    debuginfo(build-id)
    papilo-debuginfo
    papilo-debuginfo(x86-64)

papilo-debugsource:
    papilo-debugsource
    papilo-debugsource(x86-64)



Generated by fedora-review 0.10.0 (e79b66b) last change: 2023-07-24
Command line :/usr/bin/fedora-review -b 2253360
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, C/C++, Shell-api
Disabled plugins: Ocaml, SugarActivity, Python, R, PHP, Haskell, Java, Perl, fonts
Disabled flags: EXARCH, EPEL6, EPEL7, DISTTAG, BATCH

Comments:
a) An additional license needs to be specified:
Boost Software License 1.0
--------------------------
papilo-2.1.4/src/papilo/misc/extended_euclidean.hpp
This is used in:
src/papilo/presolvers/SimpleSubstitution.hpp
which is installed in libpapilo-devel
b) Builds on all non-leaf architectures:
https://koji.fedoraproject.org/koji/taskinfo?taskID=113480454
c) libpapilo does not have the license files and does not require the papilo package, perhaps it
should have the license files and the papilo package should require libpapilo?
d) The program duplicates has a generic name, but it does not match anything:
dnf provides '/usr/bin/duplicates'
Last metadata expiration check: 0:02:09 ago on Wed 14 Feb 2024 09:29:26 AM UTC.
Error: No matches found. If searching for a file, try specifying the full path or using a wildcard prefix ("*/") at the beginning.
e) Unclear why one gets:
Note: No known owner of /usr/lib64/cmake
f) Review of:
https://bugzilla.redhat.com/show_bug.cgi?id=2263821
would be appreciated if time and expertise allow

Comment 7 Jerry James 2024-02-14 22:34:23 UTC

(In reply to Benson Muite from comment #6)
> a) An additional license needs to be specified:
> Boost Software License 1.0
> --------------------------
> papilo-2.1.4/src/papilo/misc/extended_euclidean.hpp
> This is used in:
> src/papilo/presolvers/SimpleSubstitution.hpp
> which is installed in libpapilo-devel

Good catch!  Added.

> c) libpapilo does not have the license files and does not require the papilo
> package, perhaps it
> should have the license files and the papilo package should require
> libpapilo?

Yes, you are quite right.  Fixed.

> d) The program duplicates has a generic name, but it does not match anything:
> dnf provides '/usr/bin/duplicates'
> Last metadata expiration check: 0:02:09 ago on Wed 14 Feb 2024 09:29:26 AM
> UTC.
> Error: No matches found. If searching for a file, try specifying the full
> path or using a wildcard prefix ("*/") at the beginning.

That is very generic.  Do you think I should change it?  We could make it papilo-duplicates, I suppose.  I am mostly interested in the library interface, anyway, not the command line tools.

For added fun:

$ duplicates   
usage:
./check_duplicates instance1.mps instance2.mps  - check for duplicates
./check_duplicates instance1.mps                - compute unique hash for instance

So it thinks its name is "./check_duplicates"!

> e) Unclear why one gets:
> Note: No known owner of /usr/lib64/cmake

Yes.  Your package gets that, too, and both packages have a dependency on cmake-filesystem, so something broke somewhere.  I wonder if the switch to dnf5 is responsible somehow.

I have also added man pages generated by help2man.  New URLs:

Spec URL: https://jjames.fedorapeople.org/papilo/papilo.spec
SRPM URL: https://jjames.fedorapeople.org/papilo/papilo-2.1.4-1.fc41.src.rpm

Comment 8 Fedora Review Service 2024-02-14 22:45:45 UTC

Created attachment 2016743 [details]
The .spec file difference from Copr build 7010715 to 7018192

Comment 9 Fedora Review Service 2024-02-14 22:45:48 UTC

Copr build:
https://copr.fedorainfracloud.org/coprs/build/7018192
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2253360-papilo/fedora-rawhide-x86_64/07018192-papilo/fedora-review/review.txt

Please take a look if any issues were found.


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https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 10 Benson Muite 2024-02-15 06:10:48 UTC

Thanks for the fixes and adding man pages. Approved.
duplicates seems fine for now, raised an issue upstream:
https://github.com/scipopt/papilo/issues/45
Raised issue for Fedora-review:
https://bugzilla.redhat.com/show_bug.cgi?id=2264345

Comment 11 Jerry James 2024-02-16 03:10:44 UTC

Thank you for the review, Benson.  Much appreciated!

Comment 12 Fedora Admin user for bugzilla script actions 2024-02-16 03:15:32 UTC

The Pagure repository was created at https://src.fedoraproject.org/rpms/papilo

Comment 13 Jerry James 2024-02-16 03:54:49 UTC

Papilo 2.1.4 has been built for Rawhide and F40.